Variables from Prosperity Index

Clustering using gower distance

location stringency_class excess_death_class persfreedomagency Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom GovernanGovernmeffect Socialcappersonalandfamily continent population population_density median_age aged_65_older gdp_per_capita life_expectancy Climateclass cum_p_score
64 Switzerland 2 1 22.4 15.4 13.8 10.7 18.8 19.1 17.1 Europe 8715494 214.243 43.1 18.436 57410.17 83.78 Class C - Temperate (Mesothermal) Climates 0.0772404
3 Austria 2 1 22.1 14.6 13.2 12.2 17.7 17.9 16.2 Europe 9043072 106.749 44.4 19.202 45436.69 81.54 Class C - Temperate (Mesothermal) Climates 0.0845804
location stringency_class excess_death_class persfreedomagency Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom GovernanGovernmeffect Socialcappersonalandfamily continent population population_density median_age aged_65_older gdp_per_capita life_expectancy Climateclass cum_p_score
18 Egypt 1 4 8.7 14.9 12.5 0.8 2.1 7.3 9.9 Africa 104258327 97.999 25.3 5.159 10550.21 71.99 Class B - Dry (Arid and Semiarid) Climates 0.1983465
16 Denmark 2 3 22.9 16.0 13.8 11.7 19.5 18.6 18.3 Europe 5813302 136.520 42.3 19.677 46682.51 80.90 Class C - Temperate (Mesothermal) Climates 0.0071318

Pick number of clusters using the silhouette figure

2 clusters has the highest silhouette width. 3 is simpler and almost as good. Let’s pick k = 3

Interpretation

Summary of each cluster

## [[1]]
##    location         stringency_class excess_death_class persfreedomagency
##  Length:20          1:10             1:17               Min.   : 9.40    
##  Class :character   2: 4             2: 1               1st Qu.:14.70    
##  Mode  :character   3: 5             3: 2               Median :16.40    
##                     4: 1             4: 0               Mean   :16.23    
##                                                         3rd Qu.:18.07    
##                                                         Max.   :20.90    
##  Socialcapsocialnetwork healthprevent   Socialcapcivic   PersonalFreedom
##  Min.   : 8.50          Min.   : 9.20   Min.   : 4.100   Min.   : 5.40  
##  1st Qu.:12.20          1st Qu.:11.75   1st Qu.: 4.575   1st Qu.:12.38  
##  Median :13.00          Median :12.65   Median : 5.650   Median :13.45  
##  Mean   :12.92          Mean   :12.33   Mean   : 5.945   Mean   :13.84  
##  3rd Qu.:13.82          3rd Qu.:13.20   3rd Qu.: 6.825   3rd Qu.:16.07  
##  Max.   :15.80          Max.   :14.00   Max.   :10.100   Max.   :18.30  
##  GovernanGovernmeffect Socialcappersonalandfamily         continent 
##  Min.   : 5.900        Min.   :10.60              Africa       : 1  
##  1st Qu.: 9.525        1st Qu.:14.65              Asia         : 4  
##  Median :11.450        Median :15.60              Europe       :14  
##  Mean   :11.210        Mean   :15.06              North America: 0  
##  3rd Qu.:13.200        3rd Qu.:16.12              Oceania      : 0  
##  Max.   :16.000        Max.   :17.30              South America: 1  
##    population        population_density   median_age    aged_65_older   
##  Min.   :    98910   Min.   :  8.823    Min.   :26.30   Min.   : 4.489  
##  1st Qu.:  3165828   1st Qu.: 56.857    1st Qu.:37.52   1st Qu.:13.359  
##  Median :  5355002   Median : 78.841    Median :41.30   Median :15.663  
##  Mean   : 18015135   Mean   :127.877    Mean   :39.62   Mean   :15.000  
##  3rd Qu.: 12007564   3rd Qu.:123.748    3rd Qu.:43.10   3rd Qu.:18.032  
##  Max.   :145912022   Max.   :594.561    Max.   :44.70   Max.   :20.801  
##  gdp_per_capita  life_expectancy
##  Min.   : 3393   Min.   :71.45  
##  1st Qu.:11781   1st Qu.:73.68  
##  Median :21611   Median :76.47  
##  Mean   :19515   Mean   :76.36  
##  3rd Qu.:26481   3rd Qu.:78.61  
##  Max.   :35938   Max.   :83.03  
##                                         Climateclass  cum_p_score      
##                                               : 0    Min.   :-0.06918  
##  Class A - Tropical Climates                  : 1    1st Qu.: 0.10505  
##  Class B - Dry (Arid and Semiarid) Climates   : 0    Median : 0.16355  
##  Class C - Temperate (Mesothermal) Climates   :16    Mean   : 0.14279  
##  Class D - Continental (Microthermal) Climates: 3    3rd Qu.: 0.20348  
##                                                      Max.   : 0.25187  
##     cluster 
##  Min.   :1  
##  1st Qu.:1  
##  Median :1  
##  Mean   :1  
##  3rd Qu.:1  
##  Max.   :1  
## 
## [[2]]
##    location         stringency_class excess_death_class persfreedomagency
##  Length:28          1: 5             1:10               Min.   :15.00    
##  Class :character   2:14             2: 1               1st Qu.:20.02    
##  Mode  :character   3: 6             3:10               Median :21.10    
##                     4: 3             4: 7               Mean   :20.86    
##                                                         3rd Qu.:21.95    
##                                                         Max.   :23.80    
##  Socialcapsocialnetwork healthprevent   Socialcapcivic   PersonalFreedom
##  Min.   : 5.10          Min.   :12.60   Min.   : 4.100   Min.   :12.00  
##  1st Qu.:13.45          1st Qu.:13.20   1st Qu.: 6.675   1st Qu.:17.30  
##  Median :14.65          Median :13.60   Median : 9.450   Median :17.95  
##  Mean   :13.98          Mean   :13.51   Mean   : 9.357   Mean   :17.65  
##  3rd Qu.:15.70          3rd Qu.:13.82   3rd Qu.:12.200   3rd Qu.:18.43  
##  Max.   :16.40          Max.   :14.10   Max.   :14.000   Max.   :19.50  
##  GovernanGovernmeffect Socialcappersonalandfamily         continent 
##  Min.   :12.10         Min.   :12.10              Africa       : 0  
##  1st Qu.:17.68         1st Qu.:15.78              Asia         : 3  
##  Median :18.20         Median :16.20              Europe       :22  
##  Mean   :17.44         Mean   :16.18              North America: 1  
##  3rd Qu.:18.73         3rd Qu.:17.10              Oceania      : 2  
##  Max.   :19.10         Max.   :18.30              South America: 0  
##    population        population_density   median_age    aged_65_older  
##  Min.   :   368792   Min.   :   3.202   Min.   :30.60   Min.   :11.73  
##  1st Qu.:  5368528   1st Qu.:  42.753   1st Qu.:39.70   1st Qu.:15.48  
##  Median :  9167036   Median : 112.750   Median :42.60   Median :18.89  
##  Mean   : 31695700   Mean   : 443.128   Mean   :42.10   Mean   :18.31  
##  3rd Qu.: 19326875   3rd Qu.: 245.987   3rd Qu.:44.58   3rd Qu.:19.75  
##  Max.   :332915074   Max.   :7039.714   Max.   :48.20   Max.   :27.05  
##  gdp_per_capita  life_expectancy
##  Min.   :24574   Min.   :75.93  
##  1st Qu.:33987   1st Qu.:81.33  
##  Median :41622   Median :82.27  
##  Mean   :43980   Mean   :81.88  
##  3rd Qu.:47330   3rd Qu.:82.97  
##  Max.   :94278   Max.   :84.86  
##                                         Climateclass  cum_p_score      
##                                               : 0    Min.   :-0.04109  
##  Class A - Tropical Climates                  : 1    1st Qu.: 0.02111  
##  Class B - Dry (Arid and Semiarid) Climates   : 1    Median : 0.07470  
##  Class C - Temperate (Mesothermal) Climates   :22    Mean   : 0.06771  
##  Class D - Continental (Microthermal) Climates: 4    3rd Qu.: 0.10185  
##                                                      Max.   : 0.18554  
##     cluster 
##  Min.   :2  
##  1st Qu.:2  
##  Median :2  
##  Mean   :2  
##  3rd Qu.:2  
##  Max.   :2  
## 
## [[3]]
##    location         stringency_class excess_death_class persfreedomagency
##  Length:22          1:12             1: 0               Min.   : 5.70    
##  Class :character   2: 2             2:14               1st Qu.:12.25    
##  Mode  :character   3: 7             3: 4               Median :15.25    
##                     4: 1             4: 4               Mean   :14.02    
##                                                         3rd Qu.:15.88    
##                                                         Max.   :20.00    
##  Socialcapsocialnetwork healthprevent   Socialcapcivic   PersonalFreedom 
##  Min.   :10.10          Min.   : 9.80   Min.   : 0.800   Min.   : 1.700  
##  1st Qu.:14.00          1st Qu.:12.05   1st Qu.: 4.275   1st Qu.: 3.775  
##  Median :15.00          Median :13.45   Median : 6.150   Median :12.400  
##  Mean   :14.55          Mean   :12.84   Mean   : 6.027   Mean   :10.041  
##  3rd Qu.:15.50          3rd Qu.:13.70   3rd Qu.: 8.200   3rd Qu.:14.675  
##  Max.   :16.30          Max.   :14.40   Max.   :10.700   Max.   :17.500  
##  GovernanGovernmeffect Socialcappersonalandfamily         continent
##  Min.   : 5.200        Min.   : 9.70              Africa       :3  
##  1st Qu.: 8.475        1st Qu.:14.50              Asia         :9  
##  Median : 9.900        Median :15.80              Europe       :0  
##  Mean   :10.105        Mean   :15.16              North America:3  
##  3rd Qu.:11.825        3rd Qu.:16.50              Oceania      :0  
##  Max.   :15.000        Max.   :18.00              South America:7  
##    population        population_density   median_age    aged_65_older   
##  Min.   :  1273428   Min.   :   1.98    Min.   :22.90   Min.   : 1.307  
##  1st Qu.:  5895110   1st Qu.:  24.47    1st Qu.:28.12   1st Qu.: 5.205  
##  Median : 18622413   Median :  58.14    Median :30.65   Median : 6.780  
##  Mean   : 41321248   Mean   : 447.64    Mean   :31.06   Mean   : 6.909  
##  3rd Qu.: 57847957   3rd Qu.: 113.98    3rd Qu.:33.23   3rd Qu.: 8.325  
##  Max.   :213993441   Max.   :7915.73    Max.   :42.40   Max.   :12.922  
##  gdp_per_capita   life_expectancy
##  Min.   :  6253   Min.   :64.13  
##  1st Qu.: 10897   1st Qu.:73.15  
##  Median : 14814   Median :75.47  
##  Mean   : 22994   Mean   :75.33  
##  3rd Qu.: 19990   3rd Qu.:77.25  
##  Max.   :116936   Max.   :83.62  
##                                         Climateclass  cum_p_score     
##                                               : 0    Min.   :0.02013  
##  Class A - Tropical Climates                  :10    1st Qu.:0.11462  
##  Class B - Dry (Arid and Semiarid) Climates   : 9    Median :0.19834  
##  Class C - Temperate (Mesothermal) Climates   : 1    Mean   :0.19346  
##  Class D - Continental (Microthermal) Climates: 2    3rd Qu.:0.24568  
##                                                      Max.   :0.45778  
##     cluster 
##  Min.   :3  
##  1st Qu.:3  
##  Median :3  
##  Mean   :3  
##  3rd Qu.:3  
##  Max.   :3
##    location         stringency_class excess_death_class persfreedomagency
##  Length:70          1:27             1:27               Min.   : 5.70    
##  Class :character   2:20             2:16               1st Qu.:15.22    
##  Mode  :character   3:18             3:16               Median :17.60    
##                     4: 5             4:11               Mean   :17.39    
##                                                         3rd Qu.:20.88    
##                                                         Max.   :23.80    
##  Socialcapsocialnetwork healthprevent   Socialcapcivic   PersonalFreedom
##  Min.   : 5.10          Min.   : 9.20   Min.   : 0.800   Min.   : 1.70  
##  1st Qu.:12.88          1st Qu.:12.53   1st Qu.: 4.925   1st Qu.:12.40  
##  Median :14.40          Median :13.30   Median : 6.850   Median :16.00  
##  Mean   :13.86          Mean   :12.96   Mean   : 7.336   Mean   :14.17  
##  3rd Qu.:15.40          3rd Qu.:13.78   3rd Qu.: 9.100   3rd Qu.:17.70  
##  Max.   :16.40          Max.   :14.40   Max.   :14.000   Max.   :19.50  
##  GovernanGovernmeffect Socialcappersonalandfamily         continent 
##  Min.   : 5.20         Min.   : 9.70              Africa       : 4  
##  1st Qu.: 9.95         1st Qu.:14.93              Asia         :16  
##  Median :12.85         Median :16.00              Europe       :36  
##  Mean   :13.35         Mean   :15.54              North America: 4  
##  3rd Qu.:17.90         3rd Qu.:16.50              Oceania      : 2  
##  Max.   :19.10         Max.   :18.30              South America: 8  
##    population        population_density   median_age    aged_65_older   
##  Min.   :    98910   Min.   :   1.98    Min.   :22.90   Min.   : 1.307  
##  1st Qu.:  4306969   1st Qu.:  31.49    1st Qu.:32.40   1st Qu.: 8.524  
##  Median :  9167036   Median :  84.30    Median :39.65   Median :14.759  
##  Mean   : 30812139   Mean   : 354.48    Mean   :37.92   Mean   :13.780  
##  3rd Qu.: 33791678   3rd Qu.: 152.67    3rd Qu.:43.08   3rd Qu.:18.946  
##  Max.   :332915074   Max.   :7915.73    Max.   :48.20   Max.   :27.049  
##  gdp_per_capita   life_expectancy
##  Min.   :  3393   Min.   :64.13  
##  1st Qu.: 14063   1st Qu.:75.11  
##  Median : 26580   Median :78.65  
##  Mean   : 30394   Mean   :78.24  
##  3rd Qu.: 39565   3rd Qu.:82.19  
##  Max.   :116936   Max.   :84.86  
##                                         Climateclass  cum_p_score      
##                                               : 0    Min.   :-0.06918  
##  Class A - Tropical Climates                  :12    1st Qu.: 0.05075  
##  Class B - Dry (Arid and Semiarid) Climates   :10    Median : 0.11256  
##  Class C - Temperate (Mesothermal) Climates   :39    Mean   : 0.12868  
##  Class D - Continental (Microthermal) Climates: 9    3rd Qu.: 0.19609  
##                                                      Max.   : 0.45778  
##     cluster     
##  Min.   :1.000  
##  1st Qu.:1.000  
##  Median :2.000  
##  Mean   :2.029  
##  3rd Qu.:3.000  
##  Max.   :3.000

Cluster 1: 19 Countries

All Countries in Cluster 1
location excess_death_class stringency_class Climateclass
Albania 1 1 Class C - Temperate (Mesothermal) Climates
Bosnia and Herzegovina 1 1 Class C - Temperate (Mesothermal) Climates
Bulgaria 1 2 Class C - Temperate (Mesothermal) Climates
Croatia 1 1 Class C - Temperate (Mesothermal) Climates
Estonia 1 1 Class D - Continental (Microthermal) Climates
Georgia 1 2 Class C - Temperate (Mesothermal) Climates
Hungary 1 3 Class C - Temperate (Mesothermal) Climates
Kyrgyzstan 1 1 Class C - Temperate (Mesothermal) Climates
Latvia 1 1 Class C - Temperate (Mesothermal) Climates
Lebanon 1 3 Class C - Temperate (Mesothermal) Climates
Moldova 1 3 Class C - Temperate (Mesothermal) Climates
Poland 1 2 Class C - Temperate (Mesothermal) Climates
Russia 1 1 Class D - Continental (Microthermal) Climates
Serbia 1 1 Class C - Temperate (Mesothermal) Climates
Seychelles 1 4 Class A - Tropical Climates
Ukraine 1 1 Class D - Continental (Microthermal) Climates
Uruguay 1 3 Class C - Temperate (Mesothermal) Climates
Romania 2 2 Class C - Temperate (Mesothermal) Climates
Cyprus 3 1 Class C - Temperate (Mesothermal) Climates
South Korea 3 3 Class C - Temperate (Mesothermal) Climates
Cluster 1 Country counts
excess_death_class counts
1 17
3 2
2 1
stringency_class counts
1 10
3 5
2 4
4 1
Climateclass counts
Class C - Temperate (Mesothermal) Climates 16
Class D - Continental (Microthermal) Climates 3
Class A - Tropical Climates 1
continent counts
Europe 14
Asia 4
Africa 1
South America 1

Cluster 1 countries profile – other variables

  • 58% (11/19 countries) in Excess Death Class 4 (e.g. Russia, Hungary, Ukraine)

  • 63% (12/19 countries) in Stringency Class 1

  • 68% (13/19 countries) in Temperate (Mesothermal) Climates

Cluster 2: 27 Countries

Cluster 2 All Countries
location excess_death_class stringency_class Climateclass
Austria 1 2 Class C - Temperate (Mesothermal) Climates
Czechia 1 2 Class C - Temperate (Mesothermal) Climates
Israel 1 2 Class C - Temperate (Mesothermal) Climates
Lithuania 1 2 Class D - Continental (Microthermal) Climates
Luxembourg 1 1 Class C - Temperate (Mesothermal) Climates
Malta 1 1 Class C - Temperate (Mesothermal) Climates
Slovakia 1 2 Class C - Temperate (Mesothermal) Climates
Slovenia 1 2 Class C - Temperate (Mesothermal) Climates
Switzerland 1 2 Class C - Temperate (Mesothermal) Climates
United States 1 3 Class C - Temperate (Mesothermal) Climates
Portugal 2 3 Class C - Temperate (Mesothermal) Climates
Australia 3 2 Class B - Dry (Arid and Semiarid) Climates
Denmark 3 2 Class C - Temperate (Mesothermal) Climates
Finland 3 1 Class D - Continental (Microthermal) Climates
Germany 3 4 Class C - Temperate (Mesothermal) Climates
Greece 3 4 Class C - Temperate (Mesothermal) Climates
Hong Kong 3 2 Class A - Tropical Climates
Iceland 3 2 Class C - Temperate (Mesothermal) Climates
Japan 3 4 Class C - Temperate (Mesothermal) Climates
New Zealand 3 1 Class C - Temperate (Mesothermal) Climates
Norway 3 3 Class D - Continental (Microthermal) Climates
Belgium 4 1 Class C - Temperate (Mesothermal) Climates
Ireland 4 2 Class C - Temperate (Mesothermal) Climates
Italy 4 2 Class C - Temperate (Mesothermal) Climates
Netherlands 4 2 Class C - Temperate (Mesothermal) Climates
Spain 4 3 Class C - Temperate (Mesothermal) Climates
Sweden 4 3 Class D - Continental (Microthermal) Climates
United Kingdom 4 3 Class C - Temperate (Mesothermal) Climates
  • Most in Excess Death Class 1 & 2 (e.g. Russia, Hungary, Ukraine)

  • 48% in Stringency Class 3

  • 85% (23/27 countries) in Temperate (Mesothermal) Climates

Cluster 2 Country counts
excess_death_class counts
1 10
3 10
4 7
2 1
stringency_class counts
2 14
3 6
1 5
4 3
Climateclass counts
Class C - Temperate (Mesothermal) Climates 22
Class D - Continental (Microthermal) Climates 4
Class A - Tropical Climates 1
Class B - Dry (Arid and Semiarid) Climates 1
continent counts
Europe 22
Asia 3
Oceania 2
North America 1

Cluster 2 countries profile – other variables

Cluster 3: 20 Countries

Cluster 3 All Countries
location excess_death_class stringency_class Climateclass
Azerbaijan 2 3 Class B - Dry (Arid and Semiarid) Climates
Brazil 2 3 Class A - Tropical Climates
Colombia 2 3 Class A - Tropical Climates
Costa Rica 2 1 Class A - Tropical Climates
Ecuador 2 1 Class A - Tropical Climates
Guatemala 2 1 Class A - Tropical Climates
Iran 2 4 Class B - Dry (Arid and Semiarid) Climates
Mexico 2 3 Class B - Dry (Arid and Semiarid) Climates
Oman 2 3 Class B - Dry (Arid and Semiarid) Climates
Paraguay 2 1 Class C - Temperate (Mesothermal) Climates
Peru 2 1 Class A - Tropical Climates
Qatar 2 2 Class B - Dry (Arid and Semiarid) Climates
South Africa 2 1 Class B - Dry (Arid and Semiarid) Climates
Uzbekistan 2 1 Class B - Dry (Arid and Semiarid) Climates
Mauritius 3 2 Class A - Tropical Climates
Mongolia 3 3 Class D - Continental (Microthermal) Climates
Singapore 3 1 Class A - Tropical Climates
Thailand 3 1 Class A - Tropical Climates
Bolivia 4 1 Class A - Tropical Climates
Chile 4 3 Class B - Dry (Arid and Semiarid) Climates
Egypt 4 1 Class B - Dry (Arid and Semiarid) Climates
Kazakhstan 4 1 Class D - Continental (Microthermal) Climates
Cluster 3 Country counts
excess_death_class counts
2 14
3 4
4 4
stringency_class counts
1 12
3 7
2 2
4 1
Climateclass counts
Class A - Tropical Climates 10
Class B - Dry (Arid and Semiarid) Climates 9
Class D - Continental (Microthermal) Climates 2
Class C - Temperate (Mesothermal) Climates 1
continent counts
Asia 9
South America 7
Africa 3
North America 3

Cluster 3 countries profile – other variables

All 3 Clusters Profiles Together

Cluster 1 Cluster 2 Cluster 3
Number of Countries 28 21 21
Personal Freedom 16.4 21.1 15.25
Social Network 13 14.65 15
Assembly Freedom 13.45 17.95 12.4
Health Preventions 12.65 13.6 13.45
Social & Civic Participartion 5.65 9.45 6.15
Government Effect 11.45 18.2 9.9
Personal & Family Relationships 15.6 16.2 15.8
Population Density 78.84 112.75 58.14
Median Age 41.3 42.6 30.65
Aged 65 Older 15.66 18.89 6.78
GDP per capita 21610.6 41622.15 14814.22
Life Expectancy 76.47 82.26 75.47
Dominate Climate Class Temperate (21) Temperate (16) Tropical (8) & Dry (8)
Excess Death Class Class 1 (23) Class 3 (12) & Class 4 (6) Class 2 (14)
Stringency Class Class 2 (14) Class 1 (7) & Class 3 (6) Class 1 (13)

Multinomial Regression (DV – membership)

Model Summary

library(rsample)
data2$cluster <- relevel(as.factor(data2$cluster), ref = 2)
#data3 <- cbind(data2[c(2,3,17,18)], data2_mat[-1])
data_split <- initial_split(data2, prop = .75)
data_train <- training(data_split)[-1]
data_test <- testing(data_split)[-1]
library(nnet)
# Run a "only intercept" model
OIM <- multinom(cluster ~ 1, data = data_train)
## # weights:  6 (2 variable)
## initial  value 57.127839 
## final  value 57.108728 
## converged
summary(OIM)
## Call:
## multinom(formula = cluster ~ 1, data = data_train)
## 
## Coefficients:
##    (Intercept)
## 1  5.71584e-02
## 3 -8.54984e-09
## 
## Std. Errors:
##   (Intercept)
## 1   0.3381998
## 3   0.3429972
## 
## Residual Deviance: 114.2175 
## AIC: 118.2175
model <- multinom(cluster ~ ., data = data_train)
## # weights:  93 (60 variable)
## initial  value 57.127839 
## iter  10 value 34.726399
## iter  20 value 8.900943
## iter  30 value 5.284605
## iter  40 value 0.616017
## iter  50 value 0.131827
## iter  60 value 0.061905
## iter  70 value 0.024493
## iter  80 value 0.005463
## final  value 0.000075 
## converged
summary(model)
## Call:
## multinom(formula = cluster ~ ., data = data_train)
## 
## Coefficients:
##   (Intercept) stringency_class2 stringency_class3 stringency_class4
## 1   22.860238        -129.94600          1.058738        -209.86182
## 3   -4.224633           3.92066         -7.469922         -56.32008
##   excess_death_class2 excess_death_class3 excess_death_class4 persfreedomagency
## 1           -29.37746          -131.29702          -54.680141         -2.493351
## 3            44.07459            50.33522            4.881733        136.374016
##   Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom
## 1               75.66182      92.53841      18.468824        1.618292
## 3              169.31903      30.86458       6.449642     -131.393097
##   GovernanGovernmeffect Socialcappersonalandfamily continentAsia
## 1             34.149578                  -47.67178     -8.917245
## 3              1.526353                  -43.78987     51.850091
##   continentEurope continentNorth America continentOceania
## 1        11.74689              -34.90204        -1.842880
## 3       -36.57126               34.26249        -1.278195
##   continentSouth America    population population_density  median_age
## 1              0.4570643 -4.818798e-07          1.1655735    3.065139
## 3              3.6549983  7.085976e-06          0.8644428 -129.304930
##   aged_65_older gdp_per_capita life_expectancy
## 1     -30.76342    -0.06530090        3.142173
## 3    -137.71957    -0.02060771       55.873130
##   ClimateclassClass A - Tropical Climates
## 1                               -33.68206
## 3                                31.26904
##   ClimateclassClass B - Dry (Arid and Semiarid) Climates
## 1                                              -5.055084
## 3                                              13.188124
##   ClimateclassClass C - Temperate (Mesothermal) Climates
## 1                                               39.77158
## 3                                              -29.47337
##   ClimateclassClass D - Continental (Microthermal) Climates cum_p_score
## 1                                                  21.82580  -13.277662
## 3                                                 -19.20843    2.120371
## 
## Std. Errors:
##    (Intercept) stringency_class2 stringency_class3 stringency_class4
## 1 2.363847e-07      4.452977e-08      2.606673e-08      7.046433e-08
## 3 8.659380e-21      9.175819e-44      2.046525e-41      8.659380e-21
##   excess_death_class2 excess_death_class3 excess_death_class4 persfreedomagency
## 1        4.452977e-08        7.046433e-08        2.606673e-08      4.532761e-06
## 3       4.133388e-114        9.175819e-44        2.046525e-41      1.376841e-19
##   Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom
## 1           3.175240e-06  2.980414e-06   1.152044e-06    4.054232e-06
## 3           1.194994e-19  1.203654e-19   8.745973e-20    1.117060e-19
##   GovernanGovernmeffect Socialcappersonalandfamily continentAsia
## 1          3.178366e-06               3.858797e-06  1.670647e-24
## 3          9.958287e-20               1.394160e-19  1.098913e-97
##   continentEurope continentNorth America continentOceania
## 1    2.363847e-07          4.133388e-114     7.376054e-28
## 3    3.529905e-91          4.133388e-114     9.175819e-44
##   continentSouth America   population population_density   median_age
## 1           2.046525e-41 6.707649e-06       7.135551e-06 1.033972e-05
## 3           2.046525e-41 8.564992e-16       1.804216e-18 3.134695e-19
##   aged_65_older gdp_per_capita life_expectancy
## 1  4.617710e-06   6.080739e-03    1.867252e-05
## 3  7.452262e-20   2.284542e-16    6.355985e-19
##   ClimateclassClass A - Tropical Climates
## 1                             8.65938e-21
## 3                             8.65938e-21
##   ClimateclassClass B - Dry (Arid and Semiarid) Climates
## 1                                           2.046525e-41
## 3                                           2.055701e-41
##   ClimateclassClass C - Temperate (Mesothermal) Climates
## 1                                           8.892737e-08
## 3                                           4.752105e-97
##   ClimateclassClass D - Continental (Microthermal) Climates  cum_p_score
## 1                                              1.474574e-07 2.456626e-08
## 3                                              3.529903e-91 5.990356e-22
## 
## Residual Deviance: 0.0001499407 
## AIC: 116.0001

Interpretation of the Model Fit information

##                                                                                                                                                                                                                                                                                                                                   Model
## 1                                                                                                                                                                                                                                                                                                                                     1
## 2 stringency_class + excess_death_class + persfreedomagency + Socialcapsocialnetwork + healthprevent + Socialcapcivic + PersonalFreedom + GovernanGovernmeffect + Socialcappersonalandfamily + continent + population + population_density + median_age + aged_65_older + gdp_per_capita + life_expectancy + Climateclass + cum_p_score
##   Resid. df   Resid. Dev   Test    Df LR stat.      Pr(Chi)
## 1       102 1.142175e+02           NA       NA           NA
## 2        46 1.499407e-04 1 vs 2    56 114.2173 7.220232e-06

Get p-values

# Calculate z-score for the model (wald Z)
zvalues <- summary(model)$coefficients / summary(model)$standard.errors
# Calculate p-values
#pnorm(abs(zvalues), lower.tail = FALSE)*2
# 2-tailed z test
p <- (1 - pnorm(abs(zvalues), 0, 1)) * 2
p
##   (Intercept) stringency_class2 stringency_class3 stringency_class4
## 1           0                 0                 0                 0
## 3           0                 0                 0                 0
##   excess_death_class2 excess_death_class3 excess_death_class4 persfreedomagency
## 1                   0                   0                   0                 0
## 3                   0                   0                   0                 0
##   Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom
## 1                      0             0              0               0
## 3                      0             0              0               0
##   GovernanGovernmeffect Socialcappersonalandfamily continentAsia
## 1                     0                          0             0
## 3                     0                          0             0
##   continentEurope continentNorth America continentOceania
## 1               0                      0                0
## 3               0                      0                0
##   continentSouth America population population_density median_age aged_65_older
## 1                      0   0.942729                  0          0             0
## 3                      0   0.000000                  0          0             0
##   gdp_per_capita life_expectancy ClimateclassClass A - Tropical Climates
## 1              0               0                                       0
## 3              0               0                                       0
##   ClimateclassClass B - Dry (Arid and Semiarid) Climates
## 1                                                      0
## 3                                                      0
##   ClimateclassClass C - Temperate (Mesothermal) Climates
## 1                                                      0
## 3                                                      0
##   ClimateclassClass D - Continental (Microthermal) Climates cum_p_score
## 1                                                         0           0
## 3                                                         0           0

Training test accuracy %

# predicting values for train dataset
data_train$cluster_predicted <- predict(model, newdata = data_train, "class")
# building classification table
tab_train <- table(data_train$cluster, data_train$cluster_predicted)
# Calculating accuracy - sum of diagonal elements divided by total obs
round((sum(diag(tab_train))/sum(tab_train))*100,2)
## [1] 100

Test set accuracy %

data_test$cluster_predicted <- predict(model, newdata = data_test, "class")
tab_test <- table(data_test$cluster, data_test$cluster_predicted)
round((sum(diag(tab_test))/sum(tab_test))*100,2)
## [1] 55.56
## 
##  Pearson's Chi-squared test
## 
## data:  data_test$cluster and data_test$cluster_predicted
## X-squared = 7.0948, df = 4, p-value = 0.131

Exponentiate model coefficients

## extract the coefficients from the model and exponentiate
exp(coef(model))
##   (Intercept) stringency_class2 stringency_class3 stringency_class4
## 1 8.47374e+09      3.674249e-57      2.8827311489      7.213891e-92
## 3 1.46307e-02      5.043372e+01      0.0005699729      3.471380e-25
##   excess_death_class2 excess_death_class3 excess_death_class4 persfreedomagency
## 1        1.743941e-13        9.515398e-58        1.789437e-24      8.263259e-02
## 3        1.384680e+19        7.249495e+21        1.318590e+02      1.684545e+59
##   Socialcapsocialnetwork healthprevent Socialcapcivic PersonalFreedom
## 1           7.236178e+32  1.544967e+40   1.049321e+08    5.044468e+00
## 3           3.422304e+73  2.536985e+13   6.324756e+02    8.643764e-58
##   GovernanGovernmeffect Socialcappersonalandfamily continentAsia
## 1          6.775999e+14               1.978825e-21  1.340571e-04
## 3          4.601367e+00               9.600688e-20  3.297680e+22
##   continentEurope continentNorth America continentOceania
## 1    1.263602e+05           6.954010e-16        0.1583607
## 3    1.310103e-16           7.585944e+14        0.2785396
##   continentSouth America population population_density   median_age
## 1                1.57943  0.9999995           3.207762 2.143744e+01
## 3               38.66745  1.0000071           2.373683 6.975613e-57
##   aged_65_older gdp_per_capita life_expectancy
## 1  4.361310e-14      0.9367855    2.315412e+01
## 3  1.545784e-60      0.9796032    1.842435e+24
##   ClimateclassClass A - Tropical Climates
## 1                            2.355418e-15
## 3                            3.801658e+13
##   ClimateclassClass B - Dry (Arid and Semiarid) Climates
## 1                                           6.376833e-03
## 3                                           5.339854e+05
##   ClimateclassClass C - Temperate (Mesothermal) Climates
## 1                                           1.873178e+17
## 3                                           1.584454e-13
##   ClimateclassClass D - Continental (Microthermal) Climates  cum_p_score
## 1                                              3.011778e+09 1.712319e-06
## 3                                              4.548658e-09 8.334233e+00
## [1] 70